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Search Results: 1 - 10 of 39167 matches for " Sung-Gon Yi "
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Response projected clustering for direct association with physiological and clinical response data
Sung-Gon Yi, Taesung Park, Jae K Lee
BMC Bioinformatics , 2008, DOI: 10.1186/1471-2105-9-76
Abstract: We introduced a novel clustering analysis approach, response projected clustering (RPC), which uses a high-dimensional geometrical projection of response data to the gene expression space. The projected response vector, which becomes the origin in the projected space, is then clustered together with the projected gene vectors based on their different degrees of association with the response vector. A bootstrap-counting based RPC analysis is also performed to evaluate statistical tightness of identified gene clusters. Our RPC analysis was applied to the in vitro growth-inhibition and microarray profiling data on the NCI-60 cancer cell lines and the microarray gene expression study of macrophage differentiation in atherogenesis. These RPC applications enabled us to identify many known and novel gene factors and their potential pathway associations which are highly relevant to the drug's chemosensitivity activities and atherogenesis.We have shown that RPC can effectively discover gene networks with different degrees of association with clinical metadata. Performed on each gene's response projected vector based on its degree of association with the response data, RPC effectively summarizes individual genes' association with metadata as well as their own expression patterns. Thus, RPC greatly enhances the utility of clustering analysis on investigating high-dimensional microarray gene expression data with quantitative metadata.Microarray expression profiling has been widely applied to biological studies because of its ability to simultaneously examine tens of thousands of gene expression patterns. Microarray experiments have also proven to be quite useful for investigating associations between genes and physiological and clinical response measurements of many human diseases [1-3]. In particular, unsupervised learning techniques such as hierarchical clustering analysis have become one of the most commonly-used techniques for analyzing microarray data since these technique
Two-stage normalization using background intensities in cDNA microarray data
Dankyu Yoon, Sung-Gon Yi, Ju-Han Kim, Taesung Park
BMC Bioinformatics , 2004, DOI: 10.1186/1471-2105-5-97
Abstract: In this paper, we propose a two-stage method adjusting for the effect of background intensities in the normalization process. The first stage fits a regression model to adjust for the effect of background intensities and the second stage applies the usual normalization method such as a nonlinear LOWESS method to the background-adjusted intensities. In order to carry out the two-stage normalization method, we consider nine different background measures and investigate their performances in normalization. The performance of two-stage normalization is compared to those of global median normalization as well as intensity dependent nonlinear LOWESS normalization. We use the variability among the replicated slides to compare performance of normalization methods.For the selected background measures, the proposed two-stage normalization method performs better than global or intensity dependent nonlinear LOWESS normalization method. Especially, when there is a strong relationship between the background intensity and the signal intensity, the proposed method performs much better. Regardless of background correction methods used in the image analysis, the proposed two-stage normalization method can be applicable as long as both signal intensity and background intensity are available.cDNA microarrays consist of thousands of individual DNA sequences printed in a high density array on a glass slide. After being reverse-transcribed into cDNA and labeled using red (Cy5) and green (Cy3) fluorescent dyes, two target mRNA samples are hybridized with the arrayed DNA sequences or probes. Then, the relative abundance of these spotted DNA sequences can be measured. The ratio of the fluorescence intensity for each spot represents the relative abundance of the corresponding DNA sequence.In cDNA microarray experiments, there are many sources of systematic variation. Normalization is the process of removing such variation that affects the measured gene expression levels. The main idea of norm
Evaluation of normalization methods for microarray data
Taesung Park, Sung-Gon Yi, Sung-Hyun Kang, SeungYeoun Lee, Yong-Sung Lee, Richard Simon
BMC Bioinformatics , 2003, DOI: 10.1186/1471-2105-4-33
Abstract: In this paper, we use the variability among the replicated slides to compare performance of normalization methods. We also compare normalization methods with regard to bias and mean square error using simulated data.Our results show that intensity-dependent normalization often performs better than global normalization methods, and that linear and nonlinear normalization methods perform similarly. These conclusions are based on analysis of 36 cDNA microarrays of 3,840 genes obtained in an experiment to search for changes in gene expression profiles during neuronal differentiation of cortical stem cells. Simulation studies confirm our findings.Biological processes depend on complex interactions between many genes and gene products. To understand the role of a single gene or gene product in this network, many different types of information, such as genome-wide knowledge of gene expression, will be needed. Microarray technology is a useful tool to understand gene regulation and interactions [1-3]. For example, cDNA microarray technology allows the monitoring of expression levels for thousands of genes simultaneously. cDNA microarrays consist of thousands of individual DNA sequences printed in a high density array on a glass slide. After being reverse-transcribed into cDNA and labelled using red (Cy5) and green (Cy3) fluorescent dyes, two target mRNA samples are hybridized with the arrayed DNA sequences or probes. Then, the relative abundance of these spotted DNA sequences can be measured. After image analysis, for each gene the data consist of two fluorescence intensity measurements, (R, G), showing the expression level of the gene in the red and green labelled mRNA samples. The ratio of the fluorescence intensity for each spot represents the relative abundance of the corresponding DNA sequence. cDNA microarray technology has important applications in pharmaceutical and clinical research. By comparing gene expression in normal and tumor tissues, for example, microarrays
Growth hormone-releasing hormone (GHRH) polymorphisms associated with carcass traits of meat in Korean cattle
Hyun Cheong, Du-Hak Yoon, Lyoung Kim, Byung Park, Yoo Choi, Eui Chung, Yong Cho, Eng Park, Il-Cheong Cheong, Sung-Jong Oh, Sung-Gon Yi, Taesung Park, Hyoung Shin
BMC Genetics , 2006, DOI: 10.1186/1471-2156-7-35
Abstract: By direct DNA sequencing in 24 unrelated Korean cattle, we identified 12 single nucleotide polymorphisms within the 9 kb full gene region, including the 1.5 kb promoter region. Among them, six polymorphic sites were selected for genotyping in our beef cattle (n = 428) and five marker haplotypes (frequency > 0.1) were identified. Statistical analysis revealed that -4241A>T showed significant associations with CW and EMA.Our findings suggest that polymorphisms in GHRH might be one of the important genetic factors that influence carcass yield in beef cattle. Sequence variation/haplotype information identified in this study would provide valuable information for the production of a commercial line of beef cattle.The successful application of marker-assisted selection in the commercial animal population will depend on the identification of genes, including identification of genes underlying quantitative traits, exploration of genetic polymorphisms that are involved in different phenotypes of quantitative traits, and understanding how these genes/polymorphisms interact with the environment or with other genes affecting economic traits.The growth hormone (GH) is essential for post-natal growth and general metabolism, and also plays an important role in lactation. Current knowledge indicates that GH exerts a key influence in nutrient use [1], mammary development [2], and growth [3]. There have been several reports of association between quantitative traits in cattle, such as growth performance and carcass merit, and polymorphisms in the GH gene [4-6].The regulation of GH synthesis and secretion is multifactorial, but the predominant regulators of GH are the hypothalamic hormones, GH-releasing hormone (GHRH), GH secretagogue (GHS), and somatostatin (SS) [7]. In spite of the functional importance of GHRH in the regulation of GH, only one PCR-restriction fragment-length polymorphism (RFLP) [8] has been reported in cattle.In this study, we examined GHRH as one of candidate gene
Prevalence of Metabolic Syndrome according to Sasang Constitutional Medicine in Korean Subjects
Kwang Hoon Song,Sung-Gon Yu,Jong Yeol Kim
Evidence-Based Complementary and Alternative Medicine , 2012, DOI: 10.1155/2012/646794
Abstract: Metabolic syndrome (MS) is a complex disorder defined by a cluster of abdominal obesity, atherogenic dyslipidemia, hyperglycemia, and hypertension; the condition is recognized as a risk factor for diabetes and cardiovascular disease. This study assessed the effects of the Sasang constitution group (SCG) on the risk of MS in Korean subjects. We have analyzed 1,617 outpatients of Korean oriental medicine hospitals who were classified into three SCGs, So-Yang, So-Eum, and Tae-Eum. Significant differences were noted in the prevalence of MS and the frequencies of all MS risk factors among the three SCGs. The odds ratios for MS as determined via multiple logistic regression analysis were 2.004 for So-Yang and 4.521 for Tae-Eum compared with So-Eum. These results indicate that SCG may function as a significant risk factor of MS; comprehensive knowledge of Sasang constitutional medicine may prove helpful in predicting susceptibility and developing preventive care techniques for MS.
Kwang-Su Choi,Sung-Gon Kim
Acta Crystallographica Section E , 2010, DOI: 10.1107/s1600536810045101
Abstract: The title compound, C17H13ClO2, was obtained from the oxidation of 6-chloro-4-(2-phenylethenyl)chroman-2-ol, which was synthesized by the reaction of of (E)-3-(5-chloro-2-hydroxyphenyl)acrylaldehyde with styrylboronic acid using diethylamine as a catalyst. The six-membered pyranone ring of the chromane system has a screw-boat conformation. The dihedral angle between the least-squares planes of the chromane ring system and the styryl group is 85.28 (9)°.
Ki-Tae Kang,Sung-Gon Kim
Acta Crystallographica Section E , 2013, DOI: 10.1107/s1600536813006648
Abstract: The asymmetric unit of the title compound, C9H8O2, contains two independent molecules, both of which are essentially planar (r.m.s. deviations = 0.0294 and 0.0284 ). The C=C double bond is in an E conformation and the vinylaldehyde groups adopt extended conformations. In the crystal, molecules are linked by O—H...O hydrogen bonds, forming infinite chains parallel to [101].
Association of the Apolipoprotein A5 Gene ?1131T>C Polymorphism with Serum Lipids in Korean Subjects: Impact of Sasang Constitution
Kwang Hoon Song,Sung-Gon Yu,Seongwon Cha,Jong Yeol Kim
Evidence-Based Complementary and Alternative Medicine , 2012, DOI: 10.1155/2012/598394
Abstract: Apolipoprotein A5 (APOA5) was identified as a strong modulator of serum lipids. Moreover, an APOA5 gene −1131T>C polymorphism has been associated with serum lipids, but the results are inconsistent according to ethnic and racial groups. We have genotyped and analyzed 1,619 outpatients of Korean oriental medicine hospitals who were classified into three Sasang constitution groups (SCGs), So-Yang (SY), So-Eum (SE), and Tae-Eum (TE). There were no significant difference in the distribution of the APOA5 −1131T>C genotype among the three SCGs. Subjects with the C allele in SY and TE showed significantly lower serum high-density lipoprotein cholesterol (HDL-C) and higher triglyceride (TG) levels than noncarriers of the C allele. These results show the differences in the prevalence of decreasing serum HDL-C and elevating serum TG levels along with APOA5 −1131T>C polymorphism according to SCG and suggest that SCG may act as a significant risk factor for hypo-HDL-C-emia and hypertriglyceridemia susceptibility.
Characterization of SINR Region for Multiple Interfering Multicast in Power-Controlled Systems
Yi Chen,Chi Wan Sung
Mathematics , 2015,
Abstract: This paper considers a wireless communication network consisting of multiple interfering multicast sessions. Different from a unicast system where each transmitter has only one receiver, in a multicast system, each transmitter has multiple receivers. It is a well known result for wireless unicast systems that the feasibility of an signal-to-interference-plus-noise power ratio (SINR) without power constraint is decided by the Perron-Frobenius eigenvalue of a nonnegative matrix. We generalize this result and propose necessary and sufficient conditions for the feasibility of an SINR in a wireless multicast system with and without power constraint. The feasible SINR region as well as its geometric properties are studied. Besides, an iterative algorithm is proposed which can efficiently check the feasibility condition and compute the boundary points of the feasible SINR region.
A High Matrix Tolerance Cadmium Determination Method: An Analysis Method Combining Microextraction and Laser Ablation Inductively Coupled Plasma Mass Spectrometry  [PDF]
Chu-Fang Wang, Tsing Hai Wang, Yi-Jung Sung, Yi-Kong Hsieh
Journal of Geoscience and Environment Protection (GEP) , 2014, DOI: 10.4236/gep.2014.22014
Abstract: Herein, we proposed a high matrix tolerance analytical method, using a combination of ammonium pyrrolidine dithiocarbamate/methyl isobutyl ketone (APDC-MIBK) microextraction and laser ablation inductively coupled plasma mass spectrometry (LA-ICP-MS), for Cd concentration determination in aqueous samples. Only 200 μL of organic solvent was used throughout the entire analysis process, with enhancement factors as high as 25. Recoveries from replicate analyses of natural water [ NIST 1 640(a)] c ontaining m ean c oncentrations o f 3 .1 μ g C d L –1 were 95 ± 3. The corresponding Cd detection limit was 0.6 μg L–1. The main advantage of this approach is its simplicity in terms of sample preparation, as demonstrated by quantifying the Cd levels in tap water, groundwater, and seawater, using a standard addition method.
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